v1v2 (latest)

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining

28 May 2023

Jian Tang

Papers citing "A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining"

50 / 68 papers shown

Title
Recent Developments in GNNs for Drug Discovery Zhengyu Fang Xiaoge Zhang Anyin Zhao Xiao Li Huiyuan Chen Jing Li 48 0 0 02 Jun 2025
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Yang Liu Can Ma Weiping Wang 110 0 0 09 May 2025
Graph ODEs and Beyond: A Comprehensive Survey on Integrating Differential Equations with Graph Neural Networks Ziqiang Liu Xiaoda Wang Bohan Wang Zijie Huang Carl Yang Wei Jin AI4TS AI4CE 526 1 0 29 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu Jian Wu Yue Liu Mingze Yin Jieping Ye Jian Wu Zehua Wang 143 0 0 06 Mar 2025
MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra Liang Wang Shaozhen Liu Yu Rong Deli Zhao Qiang Liu Shu Wu Liang Wang MedIm 134 3 0 22 Feb 2025
SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 158 2 0 07 Dec 2024
3D Interaction Geometric Pre-training for Molecular Relational Learning Namkyeong Lee Yunhak Oh Heewoong Noh Gyoung S. Na Minkai Xu Hanchen Wang Tianfan Fu Chanyoung Park AI4CE 112 0 0 04 Dec 2024
MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild Xi Fang Jiankun Wang X. Cai Shangqian Chen Shuwen Yang Lin Yao Linfeng Zhang Guolin Ke Linfeng Zhang Guolin Ke 142 2 0 17 Nov 2024
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 149 0 0 16 Nov 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 118 7 0 14 Oct 2024
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction Jun-Hyung Park Yeachan Kim Mingyu Lee Hyuntae Park SangKeun Lee 79 0 0 09 Jul 2024
CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes Jason Yang Ariane Mora Shengchao Liu Bruce J. Wittmann A. Anandkumar Frances H. Arnold Yisong Yue 33 7 0 21 Jun 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 91 8 0 15 May 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu-Feng Li DiffM 80 1 0 09 May 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 168 25 0 01 Mar 2024
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning Rui Jiao Xiangzhe Kong Ziyang Yu Wenbing Huang Fangyuan Ren Wenjuan Tan Wenbing Huang Yang Liu 41 2 0 20 Feb 2024
A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Vignesh C. Bhethanabotla ... O. Yaghi C. Borgs A. Anandkumar Hongyu Guo J. Chayes AI4CE 82 4 0 26 Jan 2024
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 80 9 0 06 Dec 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 82 11 0 03 Nov 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 72 13 0 12 Jul 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 94 24 0 15 Jun 2023
A new perspective on building efficient and expressive 3D equivariant graph neural networks Weitao Du Yuanqi Du Limei Wang Dieqiao Feng Guifeng Wang Shuiwang Ji Carla P. Gomes Zhixin Ma AI4CE 92 41 0 07 Apr 2023
A Text-guided Protein Design Framework Shengchao Liu Yanjing Li Zhuoxinran Li A. Gitter Yutao Zhu ... Arvind Ramanathan Chaowei Xiao Jian Tang Hongyu Guo Anima Anandkumar 130 70 0 09 Feb 2023
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing Shengchao Liu Weili Nie Chengpeng Wang Jiarui Lu Zhuoran Qiao Ling Liu Jian Tang Chaowei Xiao Anima Anandkumar 135 167 0 21 Dec 2022
Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching Shengchao Liu Hongyu Guo Jian Tang 116 80 0 27 Jun 2022
A Flexible Diffusion Model Weitao Du Tao Yang Heidi Zhang Yuanqi Du DiffM 75 12 0 17 Jun 2022
Evaluating Self-Supervised Learning for Molecular Graph Embeddings Hanchen Wang Jean Kaddour Shengchao Liu Jian Tang Joan Lasenby Qi Liu 121 23 0 16 Jun 2022
Elucidating the Design Space of Diffusion-Based Generative Models Tero Karras M. Aittala Timo Aila S. Laine DiffM 277 2,035 0 01 Jun 2022
Pre-training via Denoising for Molecular Property Prediction Sheheryar Zaidi Michael Schaarschmidt James Martens Hyunjik Kim Yee Whye Teh Alvaro Sanchez-Gonzalez Peter W. Battaglia Razvan Pascanu Jonathan Godwin DiffM AI4CE 129 127 0 31 May 2022
Recipe for a General, Powerful, Scalable Graph Transformer Ladislav Rampášek Mikhail Galkin Vijay Prakash Dwivedi Anh Tuan Luu Guy Wolf Dominique Beaini 174 582 0 25 May 2022
Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations Jaehyeong Jo Seul Lee Sung Ju Hwang DiffM 90 229 0 05 Feb 2022
Direct Molecular Conformation Generation Jinhua Zhu Yingce Xia Chang-Shu Liu Lijun Wu Shufang Xie ... Tao Qin Wen-gang Zhou Houqiang Li Haiguang Liu Tie-Yan Liu 85 42 0 03 Feb 2022
Masked Autoencoders Are Scalable Vision Learners Kaiming He Xinlei Chen Saining Xie Yanghao Li Piotr Dollár Ross B. Girshick ViT TPM 507 7,865 0 11 Nov 2021
SE(3) Equivariant Graph Neural Networks with Complete Local Frames Weitao Du He Zhang Yuanqi Du Qi Meng Wei Chen Jia Zhang Tie-Yan Liu 122 84 0 26 Oct 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 113 208 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 197 321 0 07 Oct 2021
Attentive Walk-Aggregating Graph Neural Networks M. F. Demirel Shengchao Liu Siddhant Garg Zhenmei Shi Yingyu Liang 131 10 0 06 Oct 2021
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 98 40 0 30 Sep 2021
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction Xiaomin Fang Lihang Liu Jieqiong Lei Donglong He Shanzhuo Zhang Jingbo Zhou Fan Wang Hua Wu Haifeng Wang AI4CE 71 460 0 11 Jun 2021
A Variational Perspective on Diffusion-Based Generative Models and Score Matching Chin-Wei Huang Jae Hyun Lim Aaron Courville DiffM 123 195 0 05 Jun 2021
Diffusion Models Beat GANs on Image Synthesis Prafulla Dhariwal Alex Nichol 340 8,006 0 11 May 2021
Learning Gradient Fields for Molecular Conformation Generation Chence Shi Shitong Luo Minkai Xu Jian Tang DiffM AI4CE 93 216 0 09 May 2021
Graph Self-Supervised Learning: A Survey Yixin Liu Ming Jin Shirui Pan Chuan Zhou Yu Zheng Xiwei Xu Philip S. Yu SSL 123 574 0 27 Feb 2021
Self-Supervised Learning of Graph Neural Networks: A Unified Review Yaochen Xie Zhao Xu Jingtun Zhang Zhengyang Wang Shuiwang Ji SSL 158 339 0 22 Feb 2021
How to Train Your Energy-Based Models Yang Song Diederik P. Kingma DiffM 102 265 0 09 Jan 2021
Score-Based Generative Modeling through Stochastic Differential Equations Yang Song Jascha Narain Sohl-Dickstein Diederik P. Kingma Abhishek Kumar Stefano Ermon Ben Poole DiffM SyDa 486 6,599 0 26 Nov 2020
Exploring Simple Siamese Representation Learning Xinlei Chen Kaiming He SSL 266 4,082 0 20 Nov 2020
Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification Yunsheng Shi Zhengjie Huang Shikun Feng Hui Zhong Wenjin Wang Yu Sun AI4CE 116 803 0 08 Sep 2020
Denoising Diffusion Probabilistic Models Jonathan Ho Ajay Jain Pieter Abbeel DiffM 953 18,496 0 19 Jun 2020
Self-supervised Learning: Generative or Contrastive Xiao Liu Fanjin Zhang Zhenyu Hou Zhaoyu Wang Li Mian Jing Zhang Jie Tang SSL 199 1,645 0 15 Jun 2020